Spatial-linked alignment tool (SLAT) for aligning heterogenous slices.

Spatially resolved omics technologies reveal the spatial organization of cells in various biological systems. Here we propose SLAT (Spatially-Linked Alignment Tool), a graph-based algorithm for efficient and effective alignment of spatial slices. Adopting a graph adversarial matching strategy, SLAT is the first algorithm capable of aligning heterogenous spatial data across distinct technologies and modalities. Systematic benchmarks demonstrate SLAT's superior precision, robustness, and speed over existing state-of-the-arts. Applications to multiple real-world datasets further show SLAT's utility in enhancing cell-typing resolution, integrating multiple modalities for regulatory inference, and mapping fine-scale spatial-temporal changes during development. The full SLAT package is available at https://github.com/gao-lab/SLAT .

Comparative Evaluation of Standard RT-PCR Assays and Commercial Real-Time RT-PCR Kits for Detection of Lassa Virus.

Lassa virus (LASV) is a causative agent of hemorrhagic fever epidemic in West Africa. In recent years, it has been transmitted several times to North America, Europe, and Asia. Standard reverse transcription (RT)-PCR and real-time RT-PCR are extensively used for early detection of LASV. However, the high nucleotide diversity of LASV strains complicates the development of appropriate diagnostic assays. Here, we analyzed LASV diversity clustered with geographic location and evaluated the specificity and sensitivity of two standard RT-PCR methods (GPC RT-PCR/1994 and 2007) and four commercial real-time RT-PCR kits (namely, Da an, Mabsky, Bioperfectus, and ZJ) to detect six representative LASV lineages using in vitro synthesized RNA templates. The results showed that the GPC RT-PCR/2007 assay had better sensitivity compared to the GPC RT-PCR/1994 assay. The Mabsky and ZJ kits were able to detect all RNA templates of six LASV lineages. Contrastingly, the Bioperfectus and Da an kits failed to detect lineages IV and V/VI. The limit of detection for lineage I with the Da an, Bioperfectus, and ZJ kits were significantly higher than that of the Mabsky kit at an RNA concentration of 1 × 1010 to 1 × 1011 copies/mL. The Bioperfectus and Da an kits detected lineages II and III at an RNA concentration of 1 × 109 copies/mL, higher than that of the other kits. In conclusion, the GPC RT-PCR/2007 assay and the Mabsky kit were suitable assays for the detection of LASV strains based on good analytical sensitivity and specificity. IMPORTANCE Lassa virus (LASV) is a significant human pathogen causing hemorrhagic fever in West Africa. Increased traveling around the world raises the risk of imported cases to other countries. The high nucleotide diversity of LASV strains clustered with geographic location complicates the development of appropriate diagnostic assays. In this study, we showed that the GPC reverse transcription (RT)-PCR/2007 assay and the Mabsky kit are suitable for detecting most LASV strains. Future assays for molecular detection of LASV should be based on specific countries/regions along with new variants.

[Bone Marrow Osteoblasts Promotes the Proliferation Leukemia Stem Cell by Up-regulating Interleukin-1].

OBJECTIVE: To explore the extrinsic regulation mechanism of bone marrow microenvironment in leukemia cells, and investigate the promoting effect of osteoblast niche on the proliferation and self-renewal of leukemia stem cell by up-regulating the expression of interleukin-1 (IL-1) in leukemia cell. METHODS: The gene expression profiles on leukemia cells derived from AE9a mouse bone marrow endosteum and central bone marrow were determined by RNA sequencing and gene set enrichment analysis (GSEA). Quantitative real-time PCR (qRT-PCR) was used to detect the expression of IL-1 in AE9a mouse leukemia cells co-cultured with or without osteoblasts in vitro. In addition, qRT-PCR was also used to determine the expression of IL-1 in bone marrow mononuclear cell (BMMNC) from 43 patients with acute myeloid leukemia (AML). For leukemia cells co-cultured with osteoblasts or treated with IL-1ß, colony forming ability of AE9a leukemia cells was determined by colony formation assay. RESULTS: In AE9a leukemia mouse, RNA-seq data and GSEA showed that the enrichment of the upregulated genes in leukemia cells located in endosteum fell into inflammatory response gene set, among them, IL-1α and IL-1ß were significantly higher expressed in AE9a leukemia cells that located osteoblast niche (IL-1α: P<0.001, IL-1ß:P<0.001). After AE9a leukemia cells were co-cultured with osteoblasts in vitro, the expression of IL-1α and IL-1ß in leukemia cells were increased by 2.5 and 3.5 times respectively. In colony formation assay, the number of colonies was increased significantly after leukemia cells were co-cultured with osteoblasts (P<0.001). In addition, when AE9a leukemia cells were treated with IL-1ß, the number of colonies was also increased significantly (P<0.01). In AML patients, BMMNC with high percentage of CD34 positive cells exhibited higher level of IL-1 expression. CONCLUSION: Osteoblast niche can promote leukemia cell proliferation and self-renewal through up-regulating the expression of IL-1 in leukemia cells. In AML patients, the expression level of IL-1 was correlated to the percentage of CD34 positive cells in BMMNC.

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding.

Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that different omics layers typically have distinct feature spaces. Here, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic benchmarking demonstrated that GLUE is more accurate, robust and scalable than state-of-the-art tools for heterogeneous single-cell multi-omics data. We applied GLUE to various challenging tasks, including triple-omics integration, integrative regulatory inference and multi-omics human cell atlas construction over millions of cells, where GLUE was able to correct previous annotations. GLUE features a modular design that can be flexibly extended and enhanced for new analysis tasks. The full package is available online at https://github.com/gao-lab/GLUE .

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.

Single-cell RNA-seq (scRNA-seq) is being used widely to resolve cellular heterogeneity. With the rapid accumulation of public scRNA-seq data, an effective and efficient cell-querying method is critical for the utilization of the existing annotations to curate newly sequenced cells. Such a querying method should be based on an accurate cell-to-cell similarity measure, and capable of handling batch effects properly. Herein, we present Cell BLAST, an accurate and robust cell-querying method built on a neural network-based generative model and a customized cell-to-cell similarity metric. Through extensive benchmarks and case studies, we demonstrate the effectiveness of Cell BLAST in annotating discrete cell types and continuous cell differentiation potential, as well as identifying novel cell types. Powered by a well-curated reference database and a user-friendly Web server, Cell BLAST provides the one-stop solution for real-world scRNA-seq cell querying and annotation.

Novel Polymer Aerogel toward High Dimensional Stability, Mechanical Property, and Fire Safety.

Inorganc silica-based aerogels, the earliest and widely used aerogels, have poorer mechanical properties than their organic substitutes, which are flammable. In this study, a novel polymeric aerogel with high strength, inherent flame retardancy, and cost-effectiveness, which is based on poly(vinyl alcohol) (PVA) cross-linked with melamine-formaldehyde (MF), was prepared under aqueous condition with an ecofriendly freeze-drying and postcuring process. Combined with the additional rigid MF network and benifited from the resulting unique infrastructure of inter-cross-linked flexible PVA segments and rigid MF segments, PVA-based aerogels exibited a significantly decreased degradation rate and sharply decreased peak heat release rate (PHRR) in cone calorimeter tests (by as much as 83%) compared with neat PVA. The polymer aerogels have a limiting oxygen index (LOI) as high as 36.5% and V-0 rating in UL-94 test. Furthermore, the aerogel samples exposured to harsh temperatures maintain their dimensions (<10% change), original mechanical strength and fire safety. Therefore, this work provides a novel stragegy for preparing pure organic polymeric aerogel materials with high mechanical strength, dimensional stability, and fire safety.

Flame retardation of cellulose-rich fabrics via a simplified layer-by-layer assembly.

Due to the high cellulose content of cotton (88.0-96.5%), the flame retardation of cotton fabrics can be achieved via an approach for the flame retardation of cellulose. In this work, a facile water-based flame retardant coating was deposited on cotton fabrics by a 'simplified' layer-by-layer (LbL) assembly. The novel coating solution was based on a mild reaction between ammonium polyphosphate (APP) and branched polyethyleneimine (BPEI), and the reaction mechanism was studied. TGA results showed that the char residues of coated fabrics were remarkably increased. The fabric with only 5wt% coating showed self-extinguishing in the horizontal flame test, and the peak heat release rate (pHRR) in cone calorimeter test decreased by 51%. Furthermore, this coating overcame a general drawback of flame-retardant LbL assembly which was easily washed away. Therefore, the simplified LbL method provides a fast, low-cost, eco-friendly and wash-durable flame-retardant finishing for the cellulose-rich cotton fabrics.